Hi Bjoern,

This is wired. It worked before...
I will add this to the galaxy.ini in the config folder and try again.

Cheers,
Philipp

---Philipp on the road---

Am 14.06.2016 um 09:50 schrieb Bjoern Gruening <bjoern.gruen...@gmail.com 
<mailto:bjoern.gruen...@gmail.com> >:

 Hi,
 
 I don't think this will work with the script. This script reads the config 
file you specify config/galaxy.ini. And hence it needs to be added in this 
file, not via -e variables.
 This is probably something we should improve.
 
 Ciao,
 Bjoern
 
 
 > cleanup datasets error
 > 
 > HI Björn,
 > 
 > 
 > 
 > I have added these to the galaxy.ini via the docker specific e-
 > variables during startup of the container.
 > 
 > 
 > 
 > How can I check if they are broken?
 > 
 > 
 > 
 > Cheers,
 > 
 > 
 > 
 > Philipp
 > 
 > 
 > 
 > *From:*Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] *Sent:*
 > Tuesday, June 14, 2016 9:30 AM *To:* Rathert, Philipp, Dr.
 > <philipp.rath...@ibc.uni-stuttgart.de>; galaxy-dev
 > <galaxy-dev@lists.galaxyproject.org> *Subject:* Re: [galaxy-dev]
 > cleanup datasets error
 > 
 > 
 > 
 > Hi Philipp,
 > 
 > have you followed this from the readme?
 > 
 > 
 > Note that if you would like to run any of the cleanup scripts
 ><https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets>,
 > you will need to add the following to
 > |/export/galaxy-central/config/galaxy.ini|:
 > 
 > |database_connection =
 > postgresql://galaxy:galaxy@localhost:5432/galaxy| |file_path =
 > /export/galaxy-central/database/files|
 > 
 > Or is this broken? Cheers, Bjoern
 > 
 > On 14.06.2016 09:21, Rathert, Philipp, Dr. wrote:
 > 
 > Dear all,
 > 
 > 
 > 
 > when I want to start the cleanup datasets script I get the following
 > error.
 > 
 > 
 > 
 > (.venv)root@galaxy:/galaxy-central# python
 > /galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py
 > config/galaxy.ini -d -10 -1
 > 
 > Traceback (most recent call last):
 > 
 > File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py",
 > line 544, in <module>
 > 
 > main()
 > 
 > File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py",
 > line 99, in main
 > 
 > for key, value in config_parser.items( "app:main" ):
 > 
 > File "/usr/lib/python2.7/ConfigParser.py", line 642, in items
 > 
 > raise NoSectionError(section)
 > 
 > ConfigParser.NoSectionError: No section: 'app:main'
 > 
 > 
 > 
 > 
 > 
 > We are using the docker galaxy stable 16.04 version. Before this
 > script always worked without producing any error.
 > 
 > 
 > 
 > It would be great if anybody has an idea how to fix this...
 > 
 > 
 > 
 > Thank you very much in advance.
 > 
 > 
 > 
 > Cheers,
 > 
 > 
 > 
 > Philipp
 > 
 > 
 > 
 > 
 > 
 > -----Original message----- *From:* Marius van den Beek
 > <m.vandenb...@gmail.com> <mailto:m.vandenb...@gmail.com> *Sent:*
 > Tuesday 7th June 2016 14:06 *To:* Marco Tangaro
 > <ma.tang...@gmail.com> <mailto:ma.tang...@gmail.com> *Cc:* galaxy-dev
 > <galaxy-dev@lists.galaxyproject.org>
 > <mailto:galaxy-dev@lists.galaxyproject.org> *Subject:* Re:
 > [galaxy-dev] Python tool wrapper with multiple input and output
 > files
 > 
 > 
 > Hi Marco,
 > 
 > 
 > 
 > you've got an interesting use-case there.
 > 
 > You may want to use either a dataset list (if you only supply
 > rna_n.bam),
 > 
 > or a paired dataset list (rna_n.bam and dna_n.bam).
 > 
 > I would probably implement a conditional, where the user selects
 > either a dataset list or a paired dataset list.
 > 
 > The output would then be another collection of output files.
 > 
 > Have a look at the test tool folder, and see if any of the tools
 > named collection_*.xml fits what you would like to do
 > 
 > https://github.com/galaxyproject/galaxy/tree/dev/test/functional/tools
 >
 >
 > 
 These two may be a good basis for what you want to achieve:
 > 
 >https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_creates_list.xml
 >
 >
 > 
 [this one creates an output collection]
 > 
 >https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_two_paired.xml
 >
 >
 > 
 [this one has a conditional to either select a list or a paired list as input]
 > 
 > 
 > 
 > Let us know if you need more help!
 > 
 > 
 > 
 > Cheers,
 > 
 > Marius
 > 
 > 
 > 
 > On 7 June 2016 at 09:50, Marco Tangaro <ma.tang...@gmail.com
 > <mailto:ma.tang...@gmail.com>> wrote:
 > 
 > Dear experts, my name is Marco and I'm working to port our python
 > tool to the Galaxy framework. The main script needs a rna.bam file as
 > input, a reference fasta file, both mandatory. Finally, you can add a
 > dna.bam file, but this is optional. Therefore an example command is:
 > 
 > script.py -i rna.bam -f reference.fa -j dna.bam
 > 
 > The outout is a tabular. Again the -j dna.bam option is completely
 > optional. So quite soon it turned out that I had to use a python
 > wrapper to parse our script. Now the wrapper works fine.
 > 
 > 
 > The next step is to run the tool over multiple input file and we
 > would like to avoid to use a workflow.
 > 
 > The idea is that to each input file corresponds an output file. The
 > reference is still the same. For instance, we have:
 > 
 > rna_1.bam + dna_1.bam -> output_1.txt rna_2.bam + dna_2.bam ->
 > output_2.txt rna_3.bam + dna_3.bam -> output_3.txt ... and so on.
 > 
 > 
 > But I don't know the best strategy to give to my wrapper multiple
 > input files. Moreover I have to be sure, when the dna_xyz.bam files
 > are uploaded, that they correspond to the right rna_xyz.bam file.
 > 
 > I would like to have as output a page which is showing as results the
 > link to the single output files as suggested here. 
 > https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files 
 > planning to integrate a javascript interface.
 > 
 > I've browsed a lot, but on multiple input file the posts are old. I'm
 > using the last galaxy release (16_04).
 > 
 > I'm quite new to the galaxy world... Thanks a lot for your
 > suggestions, Marco
 > 
 > 
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 > 
 > 
 
 
 
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